Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Abstract

21Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei, is exceedingly 22 rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing 23 (WGS) to characterise one such unusual B. pseudomallei transmission event, which occurred between a 24 breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types 25 (STs) 259 and 261 were identified in the mother's sputum from both the primary culture sweep and in 26 purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture 27 sweeps of the mother's breast milk and the child's cerebrospinal fluid and blood samples contained only 28 ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no 29 genetic variation between mother and baby isolates, providing the strongest possible evidence of B. 30 pseudomallei transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, 31 including the mother's mixed ST-259/261 sputum sample was performed to investigate the effects of 32 mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number 33 of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of 34 incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although 35 phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results 36demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not 37 correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for 38 bacterial mixture identification and strain parsing that avoids these pitfalls. 393 Impact Statement 40Burkholderia pseudomallei is the causative agent of melioidosis, a tropical disease of high mortality. B. 41 pseudomallei infections occur almost exclusively through contact with contaminated soil and water. Using 42 whole-genome sequencing (WGS), we investigated a rare case of suspected B. pseudomallei transmission 43 from mother to child. The mother's sputum, breast milk and the baby's blood and cerebrospinal fluid (CSF) 44 specimens were collected, and DNA was extracted from both pure colonies and primary culture sweeps to 45 capture potential strain mixtures. In-depth analysis of genetic variants identified two strains in the mother's 46 sputum belonging to multilocus sequence types ST-259 and ST-261, whereas the child was infected with 47 only ST-259. Comparative genomics revealed no genetic differences between mother and child ST-259 48 isolates, providing the strongest possible evidence of transmission to the child via breast milk. The sputum 49 strain mixture was subsequently used to develop a bioinformatic method for identification and 50 quantification of mixtures from WGS data. Using this method, we found ST-259 and ST-261 at an 87%:13% 51 rat...

Genomic diversity and antimicrobial resistance of Prevotella spp. isolated from chronic lung disease airways

“…; the remaining nine contained a mixture of Prevotella and other taxa, or a mixture of multiple Prevotella spp., due to insufficient subculturing for purity prior to WGS ( Table S3 ). To avoid known bioinformatic analysis issues associated with variant calling from mixtures 46 , these mixed data were excluded from phylogenetic analysis. Among the 18 isolates, WGS identified seven Prevotella spp.…”

An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know?

“…The bacterium can either kill the human host rapidly (acute melioidosis) or hide within the host body for a long period (chronic melioidosis). With rare exceptions ( Abbink et al, 2001 ; Ralph et al, 2004 ; Aziz et al, 2020 ), B. pseudomallei is not known to transmit from person to person; indicating that B. pseudomallei has not evolved virulence mechanisms through consecutive passage in human hosts. Moreover, B. pseudomallei within-host evolution observed in chronic infections are often linked to attenuated virulence ( Price et al, 2013 ; Viberg et al, 2017 ; Pearson et al, 2020 ), which is possibly mediated by host immune evasion.…”

Development and Validation of a Burkholderia pseudomallei Core Genome Multilocus Sequence Typing Scheme To Facilitate Molecular Surveillance

“…on May 24, 2021 by guest http://jcm.asm.org/ Downloaded from Figure 2: cgMLST minimum spanning tree including isolates from a previously described human-to-human transmission event (4). Four isolates related to the transmission event (yellow) and unrelated clinical isolates sharing the same MLST ST (blue) are depicted.…”